Short-Term Dietary Intervention with Whole Oats Protects from Antibiotic-Induced Dysbiosis/Experiment 1
From BugSigDB
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Mus musculus
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Response to diet Response to diet,response to diet
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Always Dextrose Day 5 Abx
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Prophylactic oats Day 5 Abx
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Fecal pellets collected on day 5 from mice that were fed diet supplemented with oats as a preventive measure during amoxicillin treatment
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
- Group 1 sample size Number of subjects in the case (exposed) group
- 3
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- None
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- raw counts
- Statistical test
- DESeq2
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Signature 1
Source: Figure 3
Description: Differential abundance in gut microbial taxa of mice placed on whole milled oats diet with amoxicillin mitigation (Day 5) as assessed by DeSeq2
Abundance in Group 1: increased abundance in Prophylactic oats Day 5 Abx
Revision editor(s): Barrakat
Signature 2
Source: Figure 3
Description: Differential abundance in gut microbial taxa of mice placed on whole milled oats diet with amoxicillin mitigation (Day 5) as assessed by DeSeq2
Abundance in Group 1: decreased abundance in Prophylactic oats Day 5 Abx
Revision editor(s): Barrakat
